PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3651-3700 / 86044 show all | |||||||||||||||
| egarrison-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5935 | 99.4554 | 99.7320 | 55.2895 | 20089 | 110 | 20097 | 54 | 39 | 72.2222 | |
| ckim-isaac | INDEL | * | HG002compoundhet | hetalt | 88.0188 | 79.0747 | 99.2444 | 32.7152 | 19911 | 5269 | 20095 | 153 | 126 | 82.3529 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.1224 | 97.5578 | 98.6935 | 48.6222 | 20093 | 503 | 20094 | 266 | 260 | 97.7444 | |
| eyeh-varpipe | SNP | ti | map_l150_m2_e0 | * | 99.1763 | 99.6246 | 98.7319 | 78.7456 | 20435 | 77 | 20088 | 258 | 16 | 6.2016 | |
| ndellapenna-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4700 | 99.4059 | 99.5342 | 55.3861 | 20079 | 120 | 20088 | 94 | 83 | 88.2979 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.4672 | 97.2859 | 99.6775 | 38.9821 | 20037 | 559 | 20088 | 65 | 55 | 84.6154 | |
| ltrigg-rtg2 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7618 | 99.5445 | 99.9801 | 51.1635 | 20107 | 92 | 20081 | 4 | 3 | 75.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.0729 | 97.4752 | 98.6779 | 47.9442 | 20076 | 520 | 20077 | 269 | 262 | 97.3978 | |
| jpowers-varprowl | INDEL | D1_5 | HG002complexvar | het | 95.6155 | 96.8360 | 94.4254 | 57.0236 | 20108 | 657 | 20072 | 1185 | 1127 | 95.1055 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8562 | 99.7624 | 99.9502 | 47.5635 | 20151 | 48 | 20069 | 10 | 7 | 70.0000 | |
| egarrison-hhga | SNP | * | map_l150_m2_e1 | het | 99.1207 | 98.5415 | 99.7068 | 75.7393 | 20066 | 297 | 20066 | 59 | 22 | 37.2881 | |
| jli-custom | SNP | * | map_l150_m2_e1 | het | 98.8617 | 98.5267 | 99.1989 | 74.7124 | 20063 | 300 | 20060 | 162 | 49 | 30.2469 | |
| ciseli-custom | SNP | tv | map_l100_m2_e1 | * | 83.0739 | 79.3893 | 87.1172 | 73.4544 | 20072 | 5211 | 20057 | 2966 | 720 | 24.2751 | |
| gduggal-snapfb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.4947 | 99.2475 | 93.8904 | 70.4163 | 20047 | 152 | 20055 | 1305 | 194 | 14.8659 | |
| gduggal-bwafb | SNP | * | map_l150_m2_e1 | het | 98.2410 | 98.4629 | 98.0200 | 79.6828 | 20050 | 313 | 20050 | 405 | 97 | 23.9506 | |
| ltrigg-rtg2 | SNP | ti | map_l150_m2_e0 | * | 98.7701 | 97.6843 | 99.8804 | 65.6662 | 20037 | 475 | 20041 | 24 | 7 | 29.1667 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e1 | * | 95.4042 | 97.5776 | 93.3256 | 83.0965 | 20221 | 502 | 20037 | 1433 | 94 | 6.5597 | |
| jpowers-varprowl | SNP | ti | map_l150_m2_e1 | * | 97.3682 | 96.6752 | 98.0713 | 80.1400 | 20034 | 689 | 20034 | 394 | 141 | 35.7868 | |
| qzeng-custom | SNP | tv | map_l100_m2_e0 | * | 88.2470 | 80.1862 | 98.1096 | 78.5989 | 20073 | 4960 | 20033 | 386 | 305 | 79.0155 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.9631 | 97.2567 | 98.6798 | 47.9874 | 20031 | 565 | 20032 | 268 | 262 | 97.7612 | |
| gduggal-bwafb | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.3797 | 99.1386 | 99.6220 | 59.2352 | 20025 | 174 | 20030 | 76 | 54 | 71.0526 | |
| cchapple-custom | SNP | ti | map_l150_m2_e1 | * | 96.8601 | 96.7186 | 97.0020 | 78.5397 | 20043 | 680 | 20028 | 619 | 164 | 26.4943 | |
| ciseli-custom | SNP | * | map_l125_m1_e0 | het | 76.3493 | 70.6009 | 83.1168 | 80.0504 | 20045 | 8347 | 20022 | 4067 | 129 | 3.1719 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.9357 | 97.2033 | 98.6791 | 48.0009 | 20020 | 576 | 20021 | 268 | 262 | 97.7612 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5376 | 99.1089 | 99.9700 | 56.4901 | 20019 | 180 | 20019 | 6 | 6 | 100.0000 | |
| ciseli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3693 | 99.2326 | 91.7955 | 63.9797 | 20044 | 155 | 20005 | 1788 | 579 | 32.3826 | |
| asubramanian-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9233 | 98.8811 | 98.9655 | 57.0313 | 19973 | 226 | 19994 | 209 | 5 | 2.3923 | |
| bgallagher-sentieon | SNP | * | map_l150_m2_e0 | het | 98.7961 | 99.2748 | 98.3220 | 79.7541 | 19987 | 146 | 19981 | 341 | 50 | 14.6628 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e0 | homalt | 84.0977 | 72.5829 | 99.9550 | 67.6272 | 19977 | 7546 | 19977 | 9 | 8 | 88.8889 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6411 | 96.9703 | 98.3214 | 47.5930 | 19972 | 624 | 19973 | 341 | 336 | 98.5337 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 97.4077 | 95.0956 | 99.8350 | 48.2245 | 10742 | 554 | 19971 | 33 | 33 | 100.0000 | |
| hfeng-pmm3 | SNP | * | map_l150_m2_e0 | het | 99.2915 | 99.2103 | 99.3729 | 76.6202 | 19974 | 159 | 19968 | 126 | 13 | 10.3175 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.7839 | 96.9412 | 98.6414 | 47.7167 | 19966 | 630 | 19967 | 275 | 271 | 98.5455 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 61.1245 | 61.5551 | 60.6998 | 48.1943 | 13696 | 8554 | 19966 | 12927 | 11157 | 86.3077 | |
| qzeng-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.6297 | 99.6336 | 99.6257 | 58.2037 | 20125 | 74 | 19963 | 75 | 44 | 58.6667 | |
| dgrover-gatk | SNP | * | map_l150_m2_e0 | het | 98.9689 | 99.1805 | 98.7582 | 81.1353 | 19968 | 165 | 19962 | 251 | 50 | 19.9203 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6327 | 96.9169 | 98.3591 | 48.8223 | 19961 | 635 | 19961 | 333 | 328 | 98.4985 | |
| hfeng-pmm2 | SNP | * | map_l150_m2_e0 | het | 98.9416 | 99.1556 | 98.7286 | 79.5932 | 19963 | 170 | 19957 | 257 | 23 | 8.9494 | |
| gduggal-bwaplat | SNP | * | map_l125_m2_e1 | het | 80.1160 | 67.2065 | 99.1643 | 89.4169 | 19920 | 9720 | 19934 | 168 | 44 | 26.1905 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | homalt | 83.9525 | 72.3722 | 99.9448 | 68.4557 | 19919 | 7604 | 19919 | 11 | 7 | 63.6364 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 82.6699 | 77.1496 | 89.0409 | 77.8450 | 16895 | 5004 | 19914 | 2451 | 1673 | 68.2579 | |
| jlack-gatk | SNP | * | map_l150_m2_e0 | het | 93.6840 | 98.8973 | 88.9927 | 86.5727 | 19911 | 222 | 19905 | 2462 | 176 | 7.1487 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 84.8407 | 79.4106 | 91.0680 | 42.1071 | 9943 | 2578 | 19902 | 1952 | 731 | 37.4488 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e1 | * | 96.3445 | 96.0141 | 96.6772 | 77.8313 | 19897 | 826 | 19901 | 684 | 351 | 51.3158 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2176 | 96.6110 | 97.8319 | 41.8109 | 19898 | 698 | 19899 | 441 | 420 | 95.2381 | |
| ndellapenna-hhga | SNP | * | map_l150_m2_e1 | het | 98.6659 | 97.6968 | 99.6544 | 74.7044 | 19894 | 469 | 19894 | 69 | 30 | 43.4783 | |
| rpoplin-dv42 | SNP | * | map_l150_m2_e0 | het | 98.9235 | 98.8328 | 99.0144 | 75.6918 | 19898 | 235 | 19892 | 198 | 117 | 59.0909 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 63.3637 | 60.1216 | 66.9753 | 55.5677 | 18883 | 12525 | 19891 | 9808 | 7269 | 74.1130 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 63.3637 | 60.1216 | 66.9753 | 55.5677 | 18883 | 12525 | 19891 | 9808 | 7269 | 74.1130 | |
| ghariani-varprowl | SNP | * | map_l150_m2_e0 | het | 96.9127 | 98.7732 | 95.1210 | 82.9549 | 19886 | 247 | 19886 | 1020 | 198 | 19.4118 | |